Is it possible to modify the 'system bookmarks' category in the file browser?
Although I couldn't find a way to directly modify System Bookmarks, the most recent versions of Blender (2.81 and above) include an option in the Preferences that allow you to hide both the System and Recent bookmarks, which are both auto-generated bookmark types.

The options can be found in Preferences under Save &amp; Load. Check 'Hide System Bookmarks' to hide the from the file browser. You can also use 'Hide Recent Locations' if you don't like to see recent file browser history.



This does not answer the question originally asked, but it does solve the issue I was having with the bookmark sidebar having space wasted by bookmarks I didn't use.